San Pedro Bay province is relatively flat, with a bedrock of Ocala and Suwannee limestones covered by a thin layer of San Pedro clay. The clay is relatively impermeable, preventing surface water from reaching the underlying limestone. As a result, there has been little development of a karst landscape in the province, and numerous wetlands are perched on the clay. The elevation of the province ranges from 55 to 115 feet (17 to 35 m) above sea level, with a median elevation of 85 feet (26 m). It slopes down gradually from north to south, westward from the middle towards the Gulf of Mexico, and eastwards from the middle towards the Suwannee River Valley. The Econofina and Fenholloway rivers have their headwaters in the northwestern part of the province, while the Steinhatchee River arises in the southeastern part of the province. There are few or no streams elsewhere in the province.[2]
San Pedro Bay province in bordered on the north by the Madison Hills geomorphological province, along the Cody Scarp. To the east San Pedro Bay is bordered by the Branford Karst Plain province, to the southeast by the Chiefland Karst Plain province, and to the west and southwest by the Perry Karst Plain province, all of which are lower in elevantion, better drained, and have more small sinkholes then San Pedro Bay. Several streams that originate in San Pedro Bay near the Branford Karst Plain and Perry Karst Plain provinces, including the Fenholloway and Steinhatchee rivers, enter swallets shortly after leaving San Pedro Bay.[2]